Background The global prevalence of methicillin-resistant Staphylococcus aureus (MRSA) colonization in human immunodeficiency virus (HIV)-infected patients is increasing, but data about it was limited in mainland China. This study aims to investigate the epidemiology of MRSA nasal colonization among HIV-infected patients in mainland China and also evaluate the impact of methicillin-resistant coagulase-negative Staphylococci (MRCoNS). Methods This cross-sectional study was designed to collect nasal samples and individual information for HIV-infected participants. Risk factors and phenotypic and molecular characteristics among those with MRSA colonization comparing those with and without MRCoNS co-colonization were analyzed.Results We found 119 (11.89%) out of 1001 HIV-infected patients were colonized with MRSA, including 41 (4.10%) with MRCoNS and 78 (7.79%) without MRCoNS. Having a history of respiratory tract infection in the previous 6 months(adjusted OR=1.64, 95% CI: 1.04-2.57) and male gender (aOR=3.92, 95% CI: 1.20-12.85) were risk factors for the overall MRSA and MRSA without MRCoNS colonization, respectively. No risk factor was associated with co-colonization of MRSA and MRCoNS. The proportions of antibiotic resistance and toxin genes as well as the distribution of molecular types for MRSA isolates were equivalent between subjects with and without MRCoNS isolates (P-value ≥0.05). Conclusions HIV-infected patients remain a highly vulnerable population for MRSA colonization, and men and prior history of respiratory tract infection are risk factors. Risk factors and phenotypic and molecular characteristics of MRSA colonization were not affected by co-colonizing with MRCoNS.